27.08.2010 Sandra Gesing [email protected] Eberhard-Karls-Universität Tübingen A gUSE submitter for MoSGrid (Molecular Simulation Grid)

27.08.2010

Sandra [email protected]

Eberhard-Karls-Universität Tübingen

A gUSE submitter forMoSGrid

(Molecular Simulation Grid)

Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010 2

Outline• Molecular simulations• Users• MoSGrid• MoSGrid architecture• gUSE submitter• Future work

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Molecular simulations• Computational techniques• Predicting many useful functional properties of chemicals and materials

• Thermodynamic properties• Thermochemical properties • Spectroscopic properties • Mechanical properties • Transport properties • Morphological information

• Diverse fields of applications, e.g. drug designSandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010

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Molecular simulations

http://www.nmr.chem.uu.nl/haddock2.0/movies/cg1.html

Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010

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Users• Sophisticated tools and algorithms available• Scientists with different computational background• Need of self-explanatory and intuitive user

interfaces⇒ Portals


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Unifying diversity

12181 acatttctac caacagtgga tgaggttgtt ggtctatgtt ctcaccaaat ttggtgttgt 12241 cagtctttta aattttaacc tttagagaag agtcatacag tcaatagcct tttttagctt 12301 gaccatccta atagatacac agtggtgtct cactgtgatt ttaatttgca ttttcctgct 12361 gactaattat gttgagcttg ttaccattta gacaacttca ttagagaagt gtctaatatt 12421 taggtgactt gcctgttttt ttttaattgg gatcttaatt tttttaaatt attgatttgt 12481 aggagctatt tatatattct ggatacaagt tctttatcag atacacagtt tgtgactatt 12541 ttcttataag tctgtggttt ttatattaat gtttttattg atgactgttt tttacaattg 12601 tggttaagta tacatgacat aaaacggatt atcttaacca ttttaaaatg taaaattcga 12661 tggcattaag tacatccaca atattgtgca actatcacca ctatcatact ccaaaagggc 12721 atccaatacc cattaagctg tcactcccca atctcccatt ttcccacccc tgacaatcaa 12781 taacccattt tctgtctcta tggatttgcc tgttctggat attcatatta atagaatcaa

Slide copied from: Stuart Owen „Workflows with Taverna“


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MoSGridMolecular Simulation Grid (D-Grid project)Goal • Providing users with Grid services for molecular simulation tools and docking via a portal

• Implementation of high-performance computing• Workflows• Annotations of results• Data mining• Use of the D-Grid-infrastructure

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MoSGrid - Partners• Universität zu Köln• Eberhard-Karls-Universität Tübingen• Universität Paderborn• Konrad-Zuse-Zentrum für Informationstechnik Berlin• Technische Universität Dresden• Bayer Technology Services GmbH, Leverkusen• Origines GmbH, Martinsried• GETLIG&TAR, Falkensee• BioSolveIT, Sankt Augustin• COSMOlogic GmbH&Co. KG, Leverkusen Sandra Gesing - A gUSE submitter for MoSGrid – 27.08.2010

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MoSGrid - Community1. Technische Universität Chemnitz, Fakultät für Naturwissenschaften, Institut für Chemie2. International Center for Information Technology, Rheinische Friedrich-Wilhelms-Universität Bonn3. Center of Bioinformatics Saar, Universität des Saarlandes4. Institut für Physikalische und Theoretische Chemie,Technische Universität Braunschweig5. Bremen Center for Computational Materials Science, Universität Bremen6. Universität Münster, Organisch-Chemisches Institut7. Max-Planck-Institut für biophysikalische Chemie,Göttingen8. Otto-Diels-Institut für Organische Chemie, Christian-Albrechts-Universität zu Kiel9. Johann Wolfgang Goethe-Universität Frankfurt am Main,Institut für Anorganische und Analytische Chemie10. Department Chemie, Fakultät für Naturwissenschaften,Universität Paderborn11.Technische Universität Braunschweig, Institut für Organische Chemie12. Institut für Pharmazeutische Chemie, Universität Marburg13. Universität Karlsruhe (TH), Institut für Physikalische Chemie14. Albert-Ludwigs-Universität Freiburg, Institut für Anorganische und Analytische Chemie15. Max-Planck-Institut für Informatik, Saarbrücken 16. Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum 17. Department Physik, Fakultät für Naturwissenschaften, Universität Paderborn18. Lehrstuhl für Theoretische Chemie, Universität Bonn19. Institut für Physikalische und Theoretische Chemie, Universität Tübingen20. Zentrum für Bioinformatik, Universität Hamburg21. Lehrstuhl für Biophysik, Ruhr-Universität Bochum22. Department Physik, Fakultät für Naturwissenschaften, Universität Paderborn23. Johann Wolfgang Goethe Universität, Fachbereich Chemie24. Universität Rostock, Institut für Chemie, Abteilung für Anorganische Chemie25. Humboldt Universität zu Berlin, Institut für Chemie26. Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg27. Technische Universität Braunschweig, Institut für Anorganische und Analytische Chemie28. Zentrum für Bioinformatik, Universität Hamburg29. Department Chemie, Universität Hamburg30. Fachbereich Chemie - Theoretische Chemie, Technische Universität Kaiserslautern31. Fachbereich Angewandte Naturwissenschaften, Fachhochschule Gelsenkirchen32. Ludwig-Maximilians-Universität München, Department Chemie und Biochemie


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MoSGrid


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MoSGrid Components


• survey about molecular simulation tools ⇒ Gaussian, Gromacs, FlexX (to start with)• evaluation about portals ⇒ Liferay, WS-PGRADE• evaluation about workflow engines ⇒ UNICORE, WS-PGRADE• evaluation about Grid middlewares ⇒ UNICORE (D-Grid infrastructure GT 4, gLite, UNICORE)

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MoSGrid Architecture

WS-PGRADE portal(integrated workflow editor)

Hardware(local, internet or

integrated in a Grid or Cloud infrastructure)

Grid middlewareWorkflow engine

(UNICORE 6)Repository(XtreemFS)Services

Batch system

Workflow engine Repository


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gUSE submitter


Installation of WS-PGRADE portal in Tübingen• added own VO bwGRiD • submission to GT 4 ⇒ extension of existing documentation

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gUSE submitter


Available information at the beginning• József’s presentation about experiences with implementing a gUSE submitter • source code of the BES interface for P-GRADE in G3Bridge• source code of a BES submitter for gUSE (not working)• WS-PGRADE installation (without source code)

⇒ Start to implement BES submitter

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gUSE submitter


In order to test your submitter, you need 1. jdk 1.6 [on the testing machine]2. tomcat [on the testing machine]3. gUSE jar files for submitter [on the testing machine]4. your own developed submitter jar file [on the testing machine]5. appropriate configuration of your submitter [on the testing machine]6. accessing an existing and running gUSE/WS-PGRADE7. configuring gUSE/WS-PGRADE to use your submitter

For getting 1: download it from java.sun.comFor getting 2,3,5: gUSE developers can provide a prepared “submitter

package”, only a few parameters must be configured by yourselfFor getting 6: get an account from the portal operatorsFor getting 7: ask the portal operators to add your submitter to gUSE

Slide copied from József‘s presentation

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gUSE submitter


Creation of the environment under pgportal/tomcat/webapps/submitter/submitter_BES• copy submitter_local• edit of

server-config.wsdd web.xml service.properties service.xml init.jsp

• GridService interface• JobConfig class• implement Grid_BES

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GridService interface


package hu.sztaki.lpds.submitter.grids.inf;public interface GridService {

public void actionJobSubmit(String pPath,JobConfig pJC,SubmitterPortalClient pProxy);

public void actionJobAbort();public void actionJobOutput();public int actionJobStatus(); public String actionJobResource();

public void actionSetJobStatus(int pValue);

public void actionSetJobResource(String pValue);

public void setRunnerId(String pValue);

}


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JobConfig class


• JobConfig stores 3 hash tables– “Job”, “Input” and “Output” properties

• Job properties table stores property-value pairs, where– “property” is one of the job properties– “value” is a string associated to the property– “property” “value”

• e.g.: “params” ”-i input1.inp -o out1” • e.g.: “resource” “ares02.cyf-kr.edu.pl”

• Input and Output tables store key-property-value triples, where– “key” is the name of a job port– “property” is the name the property– “value” is a string associated to the property– (“key”, ”property”) (“value”)

• e.g.: (“INPORT1”,”intname”) (”input1.inp”)• e.g.: (“OUTPORT1”,”intname”) (”out1”)

• The list of properties can be found at: http://wiki.sztaki.hu/lpds/index.php/T%C3%A1tolt_adatok


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gUSE submitter


Use of source code of the provided BES submitter

• source code of GridService and JobConfig included• first compilations of Grid_BES with the result of null pointer exceptions

⇒ GridService and JobConfig not up-to-date any more⇒ import both classes from the WS-PGRADE installation as jar-files

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gUSE submitter


Use of source code of the provided BES interface for P-GRADE• in G3Bridge much more information included than the certificate, e.g. ftp user• using similar methods for BES submitter but different protocol (BFT)

⇒ need to know:The list of properties can be found at: http://wiki.sztaki.hu/lpds/index.php/T%C3%A1tolt_adatok(Hungarian comments but with examples)

Java doc (Hungarian)

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gUSE submitter


Some drawbacks occured…• my portal server was moved and not reachable for three days• needed four days to get access to a working UNICORE 6 installation• bug in the BES-UNICORE-interface for other protocols than ftp⇒ started to implement submitter_unicore

• JobConfig.class in WS-PGRADE installation not up-to-date ⇒ needed source code of JobConfig.java

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gUSE submitter_unicore


Current version• setup security (at the moment my certificate)• create UNICORE registry client• find an appropriate target system • create the job and submit it to the target system • upload executable and input files into the job directory (Uspace)• start the job • download output files (Uspace)

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Current status• jobs can be started• UNICORE returns status SUCCESSFUL• output is empty

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Next steps• fix the bug with the output• add SAML security• add generator availability• add possibility to submit UNICORE workflows

Last but not least• English Java doc• English manual

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Future work


• user-friendly parameter-sweeps• choosing of executables without uploading• reporting of intermediate results• input / output masks for executables• data management (upload, local, global)• repository of molecules and recipes• restrictions on distributing tasks (dependent on location of the data)• conversion of UNICORE workflows to WS-PGRADE workflows

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MoSGrid timeline


13.-14.09.2010 MoSGrid Meeting (presentation of submitter)

07.-09.11.2010 6. German Conference on Chemoinformatics

http://www.gdch.de/vas/tagungen/tg/5412__e.htm(MoSGrid will be introduced with link to a demonstration of the portal; later the link will

redirect to the „real“ portal) 01.12.2010 Portal-Prototype with workflow infrastructure for user community01.05.2011 Portal-Prototype with access to molecule data

repository (beta-tester)01.12.2011 Portal-Prototype with data repository and workflow infrastructure for user community01.06.2012 Portal will be released30.08.2012 End of project MoSGrid

http://www.gdch.de/vas/tagungen/tg/5412__e.htm

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Thank you for your attention.


Documents

27.08.2010 Sandra Gesing [email protected] Eberhard-Karls-Universität Tübingen A gUSE submitter for MoSGrid (Molecular Simulation Grid)